Freesurfer July 2019

freesurfer@nmr.mgh.harvard.edu

104 participants
165 discussions

Skull Strip
by Admin 03 Jul '19

03 Jul '19

External Email - Use Caution Dear Freesurfer： I am a graduate student of Northeastern University in China, and I do brain image analysis . Now,I want generated a brain mask including the brain but excluding the amplified noise regions after skull strip, but I can't find the corresponding command line, so I send this email to you, hoping to get your help. My English is poor, if I make mistakes , I hope you can understand me. Thank for your kind consideration of this request. Looking forward to receiving your reply. Thank you very much again. My Email address is:15140248156@163.com. Sincerely: Meng Nan Lin Date: 07/04/2019

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Doubts in hippocampal subfields labeling
by Antonin Skoch 03 Jul '19

03 Jul '19

External Email - Use Caution Dear experts, I noticed that systematically in most of my subjects there is area in hippocampal region, labeled in aseg as hippocampus, but NOT labeled as hippocampus in hippocampal subfields segmentation (it has zero value there). See screenshots with norm.mgz overlaid by 1) aseg, 2) hippocampal subfields segmentation. According to T1 and T2 signal, it should neither be white matter and also probably not a ventricle/CSF. Neocortex is not located here. It has similar signal intensity as hippocampus, so I think that it should be hippocampus, but I am puzzled by hippocampal subfields segmentation results there. Why it is not labeled? Could you please help me to clarify this? My concern is to correctly label this area. I could upload the example subject if it is of any help. Regards, Antonin Skoch

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Error in mris_convert thickness file from ascii format
by Jee Su Suh 03 Jul '19

03 Jul '19

External Email - Use Caution Hello, I am trying to convert ascii files containing vertex-wise thickness data into binary curvature files for subsequent smoothing and input into mri_glmfit. The command I used is: mris_convert lh.test.asc lh.test.thickness But then get the following error: ERROR: MRISalloc: nfaces=-5 < 0 No such file or directory I'm not sure what file or directory the error message is referring to, nor what the meaning of nfaces is. I am running version 6.0 on macOS Mojave. I have also attached a truncated version of the ascii file for inspection purposes (the whole thing was too big), which was converted from a csv that was generated by a python script correcting for site effects. This script took in as input the original ascii converted from the original lh.thickness file using mris_convert. The coordinates correspond to the fsaverage template (~160k vertices in the whole file). Thanks in advance for any guidance, -- JeeSu Suh, BSc. PhD. Student, Graduate Neuroscience Program McMaster University suhj5(a)mcmaster.ca

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Single SUVr for PETsurfer
by miracle ozzoude 03 Jul '19

03 Jul '19

External Email - Use Caution Hello Expert, How do i get a single SUVr value for PETsurfer? Similar to Mean_Thickness from Freesurfer, I want to extract a global/Mean SUVr value for each of my subjects. Thank you. Paul

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Qdec Message to Mailing List
by Marie Hill 03 Jul '19

03 Jul '19

External Email - Use Caution Dear Sir/Madam, Could I post the following message to the mailing list: I am running a regression testing for significant difference in cortical volume, thickness etc with 3 factors: diagnosis, genotype and gender, with age as a nuisance factor. I am using qdec but receiving Error: factor 2 must have 2 levels. Is it true that Qdec only supports factors with 2 levels? There is a page for qdec levels stating to create a file diagnosis.levels and state the three levels. I did this however the same error occurs. I was going to use glm_fit instead but I think my study isn't a linear regression so isn't suitable (as I am not interested in the change with age, just between groups). Kind regards, Marie

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Differing T1 Acquisition Comparison In Freesurfer
by Keith, Kathryn 03 Jul '19

03 Jul '19

External Email - Use Caution Hello, I’m curious if anyone has any insights about comparing T1s from different subjects that have different acquisition parameters in Freesurfer. I’m trying to get a feel for how different is too different in regards to comparing differently acquired T1s with Freesurfer. Are there any parameters that must stay consistent in order for Freesurfer to generate comparable outputs between subjects? Any other thoughts? Thank you! Kayti Keith Research Specialist I Medical University of South Carolina Department of Neuroscience Center for Biomedical Imaging 68 President Street, BE220 Charleston, SC 29425

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"MATLAB: Undefined variable" error, FSFAST Tutorial, using Octave
by Zacharie Saint-Georges 02 Jul '19

02 Jul '19

External Email - Use Caution Dear Freesurfer Developers, I am running into a "MATLAB: Undefined variable" error while doing the FSFAST tutorial, using Ubuntu 18.04, Freesurfer v6, and Octave***. I did try a few solutions posted already (please see links below), but I still cannot successfully run the tutorial command line. .basrc additions for Octave environment variables (Ref: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21241.html) export FS_OCTAVE_LIB=/usr/bin/octave export FS_OCTAVE_LIB=/usr/bin/octave additional command line: export FS_USE_OCTAVE=1 Ref: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg60448.html main command line: mkcontrast-sess -analysis my-workmem.sm05.lh -contrast encode-v-base -a 1 (tutorial page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastFirstLev… ) error output: INFO: Found 5 Non-Null Conditions INFO: Found 1 Delays Condition Weights: 1.00000000000000000000 0 0 0 0 mkcontrast2 -config my-workmem.sm05.lh/encode-v-base.config -anadir my-workmem.sm05.lh -wcond 1.00000000000000000000 0 0 0 0 -sumconds -o my-workmem.sm05.lh/encode-v-base.mat -wdelay 1 -octave $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ cmtxfile my-workmem.sm05.lh/encode-v-base.mat nconds 5, wcond 1.00000000000000000000 0 0 0 0 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau cmtxfile my-workmem.sm05.lh/encode-v-base.mat monly 0 NCond 5 WCond 1.00000000000000000000 0 0 0 0 NDelay 1 WDelay 1 TER 0.050000 sumconds 1 sumdelays 0 nircorr 0 TPreStim 0 RmPreStim 0 rdelta 0 0 rtau 0 0 ndelays 1 CNorm 1 setwdelay 0 setwcond 0 Matlab file is /tmp/mkcontrast2.18977.m MATLAB: Undefined variable. ERROR running mkcontrast mkcontrast2 -config my-workmem.sm05.lh/encode-v-base.config -anadir my-workmem.sm05.lh -wcond 1.00000000000000000000 0 0 0 0 -sumconds -o my-workmem.sm05.lh/encode-v-base.mat -wdelay 1 -octave Tue May 28 16:51:41 EDT 2019 I also modified the mkcontrast freesurfer file according to this post: Ref: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg58758.html Thank you for your assistance! Regards, Zach Zacharie Saint-Georges Research Assistant Royal Ottawa Institute for Mental Health Research Zacharie.Saint-Georges(a)TheRoyal.ca

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Converting mask.mgh to .nii
by Azeez, Azeezat 02 Jul '19

02 Jul '19

External Email - Use Caution Hello, I wish to convert a .mgh file that can be opened in AFNI I've used mri_convert , yet I am still unable to open the .nii file in AFNI. Any assistance in the matter would be greatly appreciated. Thank You, -- Azeezat Azeez PhD Student Brain Connectivity Lab Department of Biomedical Engineering || New Jersey Institute of Technology Graduate School of Biomedical Sciences || Rutgers University E: aka44(a)njit.edu

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Re: [Freesurfer] Question about OptSeq
by Greve, Douglas N.,Ph.D. 02 Jul '19

02 Jul '19

On 7/2/19 6:58 AM, Davide Nardo wrote: > > External Email - Use Caution > > Dear Prof Greve, > > I hope you don’t mind if I ask you another question. > > I assume that for the same reason (i.e., FIR analysis), null events’ > durations are multiple integers of the TR. > Actually, they are multiples of the dPSD > > But what if one wants to jitter events? > It will just put random amounts of dPSD > > Also, OptSeq does not accept --tnullmin and --tnullmax that are > different from multiple integers of the TR. > Again, the dPSD The problem with setting the dPSD to arbitrarily small values for an FIR analysis is that your statistical power drops by a factor of TR/dPSD > > Best. > > Davide > > *From:*Davide Nardo > *Sent:* 01 July 2019 18:38 > *To:* 'Greve, Douglas N.,Ph.D.' <DGREVE(a)mgh.harvard.edu> > *Subject:* RE: Question about OptSeq > > Dear Prof Greve, > > Thank you very much for your prompt and clear reply. It helps a lot!` > > Best. > > Davide > > *From:*Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu > <mailto:DGREVE@mgh.harvard.edu>> > *Sent:* 01 July 2019 15:07 > *To:* Davide Nardo <Davide.Nardo(a)mrc-cbu.cam.ac.uk > <mailto:Davide.Nardo@mrc-cbu.cam.ac.uk>>; Freesurfer support list > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > *Subject:* Re: Question about OptSeq > > No, there is not. optseq assumes you will be doing an FIR analysis > (=finite impulse response = not assuming a shape to the hemodynamic > response). In this analysis, this must be the relationship. If you > assume a shape, then this relationship is not necessary. In your case, > you can set the dPSD=1. > > On 7/1/2019 7:19 AM, Davide Nardo wrote: > > * External Email - Use Caution * > > Dear Prof Greve, > > I hope you don’t mind if I ask you a question about OptSeq. > > It looks like a constraint in using OptSeq is that any event > duration must be an integer multiple of the dPSD, which in turn > needs to be an integer multiple of the TR, and seemingly there is > no exception to this rule. > > I am in a situation in which my TR = 2 sec, and my event duration > = 3 sec, therefore I get an error message when running OptSeq. > > However, I am puzzled by this, as in my experience with fMRI an > event duration does not necessarily need to be a multiple of the TR… > > Is there any way I can circumvent this requirement in OptSeq? > > Best. > > Davide Nardo > > -- > > Davide Nardo, PhD > > MRC Cognition and Brain Sciences Unit > > University of Cambridge > > 15 Chaucer Road > > Cambridge, CB2 7EF > > Davide.Nardo(a)mrc-cbu.cam.ac.uk <mailto:Davide.Nardo@mrc-cbu.cam.ac.uk> > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. >

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Freesurfer linear mixed models - viewing results
by Mark Wagshul 02 Jul '19

02 Jul '19

External Email - Use Caution Dear FreeSurfer users/experts, I am working on a mass-univariate linear mixed effects model with cortical thickness data, with multiple time points, a cognitive measure as our primary independent variable and the usual covariates (age, gender, etc). Subject is treated as a random variable (i.e. the first column of all ones is the random variable "Zcols"). We have run through the first few steps to produce the covariance matrices, and note a number of clusters of significance using the "patch" function with the results projected onto lhsphere. We would like to view these results in a more conventional manner, e.g. projected onto the inflated cortex of fsaverage. Is this possible? Thanks for any advice you can provide. Best, Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einstein.yu.edu<mailto:mark.wagshul@einstein.yu.edu> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

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Freesurfer July 2019